ATLANTIS. Rodney McKay, Aidan Ford, Doctor Zelenka and another man called Hays are checking out one of the piers of Atlantis after the flooding caused by the hurricane. The corridors in that area are quite dark, so they all have torches.
ZELENKA: Seven thousand, five hundred forty-nine.
McKAY (sarcastically): Oh, please. Prime. Four thousand and twenty-one.
ZELENKA: Ah, nice try! Uh, not prime. OK – Lieutenant Ford: five hundred ninety-nine.
FORD: I don’t care if it’s a prime number or not.
ZELENKA: Oh, come on. Yes or no?
FORD (clearly guessing): No.
ZELENKA (to Rodney): Ha! It’s incredible! Ten for ten!
McKAY: He is terrible.
FORD: So I suck at Prime/Not Prime. Somehow I’m going to sleep tonight.
ZELENKA: At this point it’s gone way beyond you not knowing your prime numbers.
McKAY: It’s a true/false game. Statistically, just by guessing, you should be getting at least half of these right. Look: nine ninety-three.
FORD (guessing): Prime.
McKAY: Oh, come on, that’s an easy one! You hearing this, Hays?
HAYS (bored): Not really. Guess I’ve been too busy doing my job.
McKAY: We’ve already been through this section of Atlantis, Doctor Killjoy. It’s structurally sound.
ZELENKA: Lieutenant Ford, would you mind being a subject of research paper on statistical probabilities? (He giggles.)
(Aidan, fed up and embarrassed, rounds on Zelenka.)
FORD: This is some sort of pay-back for guys like me beating up guys like you in high school, right? (He glares at Zelenka for a moment, then turns and stomps off. Zelenka stands there, startled, for a moment, then follows the others down the corridor to meet up with various other groups of personnel who have been investigating the area. At around that time, Elizabeth Weir contacts Rodney by radio from the Control Room.) [Note: in this episode a lot of people are wearing earpiece/microphone combinations rather than speaking into hand-held radios, so a comment of “(over radio)” doesn’t mean that the person lifts a radio and speaks into it.]
WEIR: So, Rodney, what’s it like out there in the suburbs today?
McKAY: Essentially, with the exception of the upper level Storage Room, which the lovely and talented Dumais informs me is in no immediate danger, this pier’s in relatively good shape.
(Dumais and her team are just returning to the rendezvous point at that moment.)
WEIR: Even after all the flooding from the storm?
McKAY: Well, it’s dark, it’s damp and it smells terrible, but from an engineering standpoint we’re good.
WEIR: Head back.
McKAY: Heading back. (He turns to face the group of people around him.) Alright, you clowns, listen up! I don’t often get a chance to say this, so savour it: good work, boys and girls! Let’s go home.
ZELENKA (looking around): Wait, wait, wait. We’re missing Johnson and Wagner.
(Rodney sighs irritably and activates his radio.)
McKAY: Wagner, Johnson, what’s your position?
(There’s a long silence, then Wagner’s voice comes over the radio. He sounds terrified.)
WAGNER: We need back-up! They’re coming at us!
McKAY: What?!
FORD: (to Zelenka): Where are they?
(Zelenka checks his lifesigns detector.)
ZELENKA (indicating the way): Down this corridor.
McKAY (into radio): We’re on our way.
(Everybody rushes down the corridor until they reach Wagner and Johnson. Wagner is lying on the floor. Johnson is sitting on the floor against a wall with her legs drawn up and her head down on her knees. Rodney rushes over to her.)
McKAY: Johnson, Johnson, you OK?
(Aidan goes to Wagner and checks his pulse.)
FORD: McKay. (Rodney looks over to him.) He’s dead!
McKAY: Johnson, what happened here?
JOHNSON (crying, without looking up): They got him.
McKAY: Who got him?
(Johnson looks up and stares in terror over Rodney’s shoulder before scrambling to her feet and starting to back away.)
McKAY: Calm down. There’s nothing here.
(Johnson continues backing away, now flailing at something only she can see.)
JOHNSON: Can’t you see them? They’re everywhere!
McKAY (into radio): Beckett, I need a medical team down here, stat!
(Johnson is still trying to fight off whatever she can see. Zelenka and Hays rush to hold her, trying to calm her down. After a moment, her legs buckle under her. As Zelenka and Hays lower her carefully to the ground, she clutches at her head, then screams in anguish for several seconds before going limp. Zelenka brushes her hair away from her face and puts his fingers to her neck. We see that there is blood coming from her nose and mouth. Zelenka looks up at Rodney, bewildered.)
ZELENKA: It’s no use. She’s gone.

MEDICAL LAB. Carson Beckett replies to Rodney.
BECKETT (into comms): McKay, this is Doctor Beckett. What exactly is the nature of the emergency?
(Back in the corridor, Wagner’s and Johnson’s bodies are being covered over.)
McKAY (into radio): It’s too late. They’re gone.
BECKETT: Who’s gone? How?
McKAY: Wagner and Johnson. I need a containment team here.
BECKETT: I’m sorry?
FORD (to Rodney): A containment team? Why?
McKAY: People don’t just see things and drop dead, Lieutenant. We spent the last hour surveying unexplored areas of this city. I think Wagner and Johnson were exposed to something.
FORD: Yeah, but ...
McKAY: And if they were infected, there’s a very good chance that we were too.
ZELENKA: I recommend a Level Four quarantine until we know what we’re dealing with.
McKAY: Agreed. (Into radio) Carson, you hear all that?
BECKETT: Aye. We’ll get to the hazmat gear and head down. Sit tight. I’ll make sure Doctor Weir’s briefed.
McKAY: Thank you very much.
BECKETT (to his staff): OK, you heard the man. Follow me, ladies and gentlemen.

CORRIDOR.
PETERSON: So, wait, what, we’re just gonna stay here?
McKAY: That’s the plan, yes.
PETERSON: May I say it’s a terrible one?
McKAY: No, you may not.
PETERSON: I think we should get the hell out of here.
ZELENKA: If it is an airborne agent, we may already be infected. Heading back to the city would only endanger the rest of the population.
PETERSON: What if we’re not infected yet?
McKAY: Well, there’s no way of knowing.
PETERSON: But I feel fine. I feel perfectly fine!
McKAY: End of discussion. Peterson, we’re staying here. Actually – wait a second ... (He snaps his fingers several times as he formulates an idea.) Everyone follow me. (He heads off and gradually all the others follow him. Peterson hangs back and turns as if to go in another direction but finds two marines standing behind him. One of them smiles at him mock-sweetly. Peterson reluctantly turns again and follows the others.)

ELIZABETH’S OFFICE. Peter Grodin is bringing Elizabeth up to date with developments.
GRODIN: They’ve begun to institute a Level Four quarantine.
WEIR: It can’t really be a biological infection, can it?
GRODIN: I have no idea what it is, but I agree we should play it safe and initiate self-regulated quarantine in all populated sections of the city.
WEIR: That’s pretty severe.
GRODIN: We’ve known for some time that the Ancients suffered from a plague. If McKay and his team have somehow stumbled upon it and become infected, we’ll need to take every precaution to prevent an outbreak.
WEIR: Alright. We will suspend any and all Gate activity and keep everyone where they are. Again, just until we have a clearer picture of exactly what it is that killed Wagner and Johnson.

GYM. (Or a room that has been designated the gym.) John is twirling two Athosian fighting sticks. Opposite him, Teyla stands with two sticks in one hand. She looks very relaxed, while John is concentrating hard. He runs forward and strikes at her with both of his sticks but she easily fends them off with just one hand and – to add insult to injury (or rather, injury to insult) – steps casually past him and smacks him none too gently on the backside with her sticks. John grimaces and limps round to face her again. Again he attacks her and again she easily meets every move he attempts. This continues for a minute or two until finally Teyla tires of playing with him, smacks one stick out of his hand, hits him in the back of the knees to make him fall and drop the other stick, then stands behind him and holds him tightly across the neck with her sticks.
TEYLA (sternly): You have not been practising.
SHEPPARD: Yes I have.
TEYLA: If this was really a fight ...
SHEPPARD: If this was really a fight, I would have shot you by now. (Exasperated, Teyla releases her grip around his neck and shoves him to the floor.) Y’know, no matter how many hours I put into this, you’re still gonna kick my ass.
TEYLA: It is not for the winning that we practise.
SHEPPARD: Well, what’s the point?
(They go over to a bench, collect their bags and walk towards the exit. Just then, there is a beeping noise and then Elizabeth’s voice comes over the comms.)
WEIR: May I have everyone’s attention please? We have run into a questionable medical situation and at Doctor Beckett’s suggestion we have decided to put the city into a self-regulated quarantine. For at least the next couple of hours, I need everyone to stay where they are, and report anyone moving freely through the halls. I hope you’ll understand. Thank you.
SHEPPARD: What the hell is this? (He rummages through his bag but can’t find what he wants. He turns to Teyla.) Did you bring your radio?

CORRIDORS. Rodney and the others are walking through the corridors.
FORD: Isn’t this the same section Johnson and Wagner were exploring?
McKAY: Yes.
FORD: So we’re retracing their steps.
McKAY: That’s right. Don’t worry, my motivations are based entirely on self-preservation.
PETERSON: Wait, wait, wait! Wait! Ford’s right. Doesn’t this increase our chances of getting infected?
(Rodney stops walking and turns to face everyone else.)
McKAY: Alright, let me spell this out for you, OK? If there is a bacterial agent and it is not airborne, then it should be relatively safe for us to look around as long as we take the proper precautions. However, if it is an airborne agent, then there’s a very good chance we’ve already been infected.
FORD: Well, shouldn’t we wait for Doctor Beckett to decide that?
McKAY: Those men were only down there for twelve hours. Even if they were infected right away, that’s an alarmingly short incubation period. Now, if anyone else is infected – as in, I don’t know, maybe us – seconds are gonna count, Lieutenant. Alright. (He holds out his hand.) Light. (Zelenka hands him a torch.) Let’s go. (He heads off again.)

LATER. The team come to a partially open doorway. Peering inside, Rodney sees that it’s a lab of some kind.
McKAY: Right, everybody stay here. Ford ...
FORD (who was already turning away): You just told me to ...
McKAY: Everybody except Ford stay here. You think I’m going in there by myself? Uh-uh. (He and Aidan squeeze through the doorway and go inside the lab. Their feet crunch through broken glass.) Don’t touch anything. (They go over to some large glass jars on a central table. Several of them are broken.) This is not good.

GYM. Teyla obviously did have her radio because John is now arguing with Elizabeth, who is still in the Control Room. She has Sergeant Bates with her.
SHEPPARD: I’m ranking military officer here.
WEIR: Yes, I’m aware of that, Major. You were off radio and we had to act quickly. Now, this is all protocol that was put into place long before this expedition began. Bates is here with me and we agreed this was the best plan of action.
SHEPPARD: Alright, alright. Teyla and I are coming up to join you.
WEIR: We’re in a self-regulated quarantine, Major. Everyone stays where they are.
SHEPPARD: We’re nearly a mile away on the east pier. D’you really think I’m in any sort of danger walking from here to the Control Room?
WEIR: At this point we don’t know where they contracted the virus. This is a medical situation, John. Only authorised personnel in hazmat suits are allowed to roam freely – those rules apply to everyone, including you.
SHEPPARD (slowly, as if explaining it to an idiot): Well, then, get someone to bring me a hazmat suit.
WEIR (starting to get angry): Everyone in hazmat is busy configuring the lab to deal with a possible outbreak. Now if an opportunity arises, I will send somebody to come get you, but in the meantime, radio contact will have to do.
SHEPPARD (frustrated): Alright. Just ... keep us in the loop.
WEIR: Will do.
(Irritated, John walks back to the bench and tosses his bag down. Teyla rolls her eyes slightly.)

ANCIENT LAB. The rest of Rodney’s team have now come in and are looking at the damage. Some of them have set up laptops.
ZELENKA: Any number of these smashed and open containers could have released the virus that killed Johnson and Wagner.
FORD: And how would something like that survive for all these years?
DUMAIS: Viruses can remain dormant for long periods.
ZELENKA: I’m hoping the answer will be found in the database. (He walks over to a console, where Rodney is already working.) OK, I think that we ...
McKAY (holding up his hand): Yes, yes, yes, yes, yes. It doesn’t appear to be networked in with the rest of the Ancient systems. In fact, if you look, it only contains information about the experiments that took place in this room. (He realises something and slaps his radio to activate it.) Weir, it’s McKay.
WEIR: Go ahead, Rodney.
McKAY: Where’s Beckett?
WEIR: He’s on his way. It takes some time to load a whole medical team into suits.
McKAY: Well, we seem to have stumbled across something that I find ... a little troubling.
WEIR: That’s not what I wanted to hear.
McKAY: I think we may have found an Ancient viral lab. Wagner and Johnson must have been exposed here. Now, it’ll take weeks to sift through all this data, and there’s no way of knowing whether the Ancients were just studying the viruses or actively creating them. (Behind him, Dumais looks up from her laptop, suddenly terrified.) Either way, the storm’s done quite a number on this place and I’ve got ... (Dumais starts whimpering in terror, staring at something only she can see. Rodney hears her and turns around.) Dumais. Dumais? (She holds up her hands to try to prevent whatever it is from getting to her.) Dumais!
(Dumais turns to look at Peterson standing beside her. She rushes towards him.)
DUMAIS: It’s all over you! (She starts flailing at him, trying to brush something off him.)
PETERSON: Dumais? Dumais! (He tries to fend her off.)
DUMAIS: They’re all over you! They’re all over you!
(Rodney rushes over and tries to pull her off Peterson. Zelenka comes over to help. Dumais screams and clutches her head, just like Johnson did, then grunts and starts to convulse.)
(Nearby, Peterson is watching what’s happening, then glances away and stares terrified at a wispy, Wraith-like apparition – except this looks a lot darker and scarier than the Wraith ‘ghosts’. He flinches away as it rushes towards him ... and then it disappears.)
(Meanwhile, Dumais is alternating between grunting in pain and screaming. With everybody distracted by her, Peterson turns and quietly slips away.)
(McKay and Zelenka lower Dumais to the floor. There is blood coming from her nose, mouth and ears. Zelenka checks her pulse, then looks up at Rodney and shakes his head. Nobody except the viewers hears Peterson’s footsteps receding as he runs away.)
McKAY (into radio): Tell Beckett to pick up the pace – I’ve just lost another member of my team!
(Aidan stares in disbelief at the scene before him, then looks around.)
FORD: Where’s Peterson?
McKAY: What?
FORD: Peterson!

LATER. Some distance away, Peterson is hurrying along a corridor. In the Control Room, Elizabeth and Sergeant Bates are looking at a screen which shows lifesigns movements in the corridors.
WEIR: Yes, OK, I think we have him. He’s trying to make his way back. It should be OK – Grodin is locking all the doors in the hallway and killing power to the entire section.
McKAY: You need to send someone to stop him.
WEIR: It’s under control, Rodney.
McKAY: No, Elizabeth, it’s not under control. He knows almost as much about Ancient technology as I do. At the very most, what you’re doing will just slow him down.
(Peterson has reached a sealed doorway. He has opened the door panel and is tinkering with the crystals inside. Moments later, the door opens a little. Painfully, he squeezes through the gap and continues on.)
(In the Control Room, Weir and Bates watch as Peterson’s signal moves on.)
WEIR: Where does that hallway lead?
GRODIN: Straight here.

Peterson reaches another sealed doorway and prises the cover off the door panel. He jumps as Elizabeth’s voice comes over the comm system.
WEIR: Peterson? This is Elizabeth Weir. Can you hear me? I can’t imagine how frightening this whole ordeal must be, but Doctor Beckett has reached the rest of your team and begun to treat them. (Peterson carries on working on the door panel.) Now, I think the best thing for you to do is to head back. If Beckett gives you a clean bill of health, we’ll make sure you get back to the city as soon as possible. (Peterson succeeds in getting the door to open a little. He squeezes through the gap. In the Control Room, Weir sees his signal move on. She turns to Peter.) Are you sure he can hear me?
GRODIN: Positive.
WEIR: Can you do anything to make it harder to get through those doors?
GRODIN: I can try. (He starts working on his console as Elizabeth and Bates anxiously watch Peterson’s signal getting closer to the Control Room.)

ANCIENT LAB. Beckett’s team has indeed arrived, each of them wearing hazmat suits. They are checking various people out. Carson is taking Rodney’s blood pressure.
BECKETT: Well, you seem perfectly fine.
McKAY: Well, Dumais seemed fine, right up to the point where she wasn’t.
BECKETT: I’ve had them set up a small field station down the corridor. We’ve already started the autopsies.
McKAY: Any ideas?
BECKETT: From what we can tell, you’re all in good shape, so I wouldn’t jump to any conclusions.
McKAY (irritably): Stop trying to convince me I’m fine, Carson. I think we all know better.
BECKETT: I was just trying to ...
McKAY: Are we done here?
BECKETT: Yes.
(Rodney pulls the blood pressure cuff off his arm.)
McKAY: I’m gonna see what I can get from the database. Let me know what the autopsy shows up.
BECKETT: Alright.
McKAY: Oh – and tell your pathologists to start with their heads.
(Carson nods and walks away. Rodney walks over to the Ancient console, but then stops and turns around slowly. He can see something flitting around the room. (We don’t see what it is, but Rodney’s head and eye movements indicate that he’s watching something.) Nearby, one of the medical team has put a thermometer in Zelenka’s ear. Zelenka sees what Rodney is doing and pulls his head away from the medic, looking at Rodney in concern. After a moment, Rodney stops seeing whatever it was and turns back to the console, but then turns back and looks nervously around the room before getting back to work.)

GYM. John and Teyla are sitting on the bench.
SHEPPARD (into radio): Someone has to do something.
WEIR: We are doing something. (In the Control Room, Peter is moving small glass plates on a console into different positions.) Grodin’s working on a plan to limit the door controls ...
SHEPPARD (interrupting): That’s not good enough. Someone has to go out there and stop him. Teyla and I are ready.
WEIR: Major, we’ve been ...
SHEPPARD (interrupting again): Peterson obviously isn’t thinking straight and he’s endangering the entire population of the city.
WEIR: We don’t yet know the nature of the virus we’re dealing with. This is still a medical situation.
SHEPPARD: Oh, we don’t have time for this. I’m heading out. (He stands up.)
WEIR: Grodin, seal the gym.
(Peter presses buttons on his console. As John walks towards the doors of the gym, they close just before he can reach them.)
SHEPPARD: What the hell is this?
WEIR: You said so yourself – you are the ranking military officer. I can’t chance you getting infected.
SHEPPARD: I can’t chance you getting infected. Bates?
BATES: Yes, sir.
SHEPPARD: Unlock the gym.
BATES: Yes, sir. (He walks towards the console.)
WEIR: Stand down, Bates. (Into comms) You are not in command here, Major.
SHEPPARD: Well, we’ll agree to disagree. Bates, open the door.
(Bates looks at Elizabeth for a moment, then steps forward again.)
WEIR (firmly): Don’t.
(Bates stops again.)
SHEPPARD: Elizabeth, he’s heading right for you.
WEIR: So we’ll stop him. We’ll talk him down, we’ll block his way, we’ll ...
SHEPPARD: Sergeant Bates, I am ordering you to open up the doors between the gym and the med lab right now.
(In the Control Room, Elizabeth and Bates commence a stare-down. Bates’ expression is resolute; Elizabeth is trying to look firm but she’s clearly afraid that he is going to disobey her in favour of his commanding officer.)
(In the gym, a few seconds later the doors slide open.)
SHEPPARD: We’re heading out. (He runs off. Teyla grabs her bag and follows.)
(In the Control Room, Bates is unsuccessfully trying to hide his smug expression.)
BATES: I’m sorry, ma’am.
WEIR: Doesn’t really matter now, does it?

FIELD STATION. Behind protective plastic sheeting, Doctor Biro is preparing to start her final autopsy. Just outside, the other two bodies are in body bags.
BIRO (into radio): Doctor Beckett, I have the preliminary autopsy results from the first two victims, sir.
BECKETT: Anything of interest?
BIRO: They both died of a ruptured sacular brain aneurysm – which, in itself, isn’t all that remarkable. I mean, sure, the chances of two people standing next to each other and dying of it is statistically improbable, yes, but it’s not the smoking gun we were hoping for, cos I know you said ...
BECKETT (interrupting): Get to the good part, Doctor Biro.
BIRO: Yeah, sorry, sir. (Standing next to Carson, Rodney twirls his hand in a ‘get on with it’ gesture.) What is truly interesting is that both ruptures happened in exactly the same place, right above the visual cortex.
BECKETT: And the third one, Dumais?
BIRO: Just getting to her now, sir. (She starts up a high-pitched drill.) I’ll let you know.
McKAY: She did say brain aneurysm, right?
BECKETT: That’s right.
McKAY: That’s the best news I’ve heard all day. Let me show you something.

MEDICAL LAB. John and Teyla are getting into hazmat suits.
TEYLA: You should not have undermined Doctor Weir’s authority in front of Sergeant Bates.
SHEPPARD: Sometimes Elizabeth makes a decision early on and gets locked into it. That’s a problem.
TEYLA: She is not the only one who suffers from that affliction.
(John looks at her, then rolls his eyes before activating his radio.)
SHEPPARD: Doctor Weir, this is Sheppard. Teyla and I are ready to head out. What’s Peterson’s location?
(In the Control Room, Elizabeth hears him but stares at a laptop and does not reply.)
SHEPPARD: Elizabeth.
(Elizabeth pauses for a moment longer, then speaks, her voice flat and emotionless.)
WEIR: He’s in section E19, level three.
(John puts his hazmat helmet on and looks at Teyla.)
SHEPPARD: Let’s head out.

SECTION E19, LEVEL 3. Peterson is working on another door panel. The door opens a fraction and Peterson struggles to push it open wide enough to be able to squeeze through. After a second, however, he stops pushing and turns around, terrified, as a dark, misty, ghostly figure rushes towards him. There’s a hint of a skeletal face in the mist. The ghost is emitting a high-pitched screech. Peterson screams and tries to fend it off. A moment later, however, he stops screaming and looks around nervously – the ghost is gone. He gets back to forcing the door open and squeezes through. He looks back briefly into the hallway he just left to see if the ghost is still around but there’s no sign of it. He runs off.

ANCIENT LAB. Rodney opens a laptop and shows the screen to Carson.
McKAY: I’ve read the entire entries – it’s incredibly long, but this looks like our guy. Six hour hibernation, reoccurring visions, and best of all, so I’ve left it til last, brain haemorrhage, or aneurysms.
BECKETT: That definitely sounds familiar.
McKAY: Maybe there’s something in here about how to ... (He trails off and looks up, afraid. The dark ghostly mist comes out of the wall behind Carson. Rodney screams and ducks down. Everybody turns round to look at him. Rodney straightens up again, looking around the room, but there’s no sign of the ghost. His voice is a whimper as he speaks.) Sorry.
BECKETT: Rodney?
McKAY (reluctantly): I’ve been seeing things.
BECKETT: Since when?
McKAY: About an hour. First you think it’s just your eyes playing tricks on you but eventually ...
(Hays, recognising what Rodney is describing, steps forward.)
HAYS: ... they get worse.
McKAY: You too?
(Hays nods and looks at Carson.)
HAYS: They come right at you.
McKAY: It’s like a ghost.
ZELENKA: I’ve been going over the survey schedule. Johnson and Wagner started off on their own, but then crossed paths with Dumais an hour later.
BECKETT: Dumais died almost exactly an hour after Johnson and Wagner. Who did they meet up with next?
ZELENKA: My greater concern is who Dumais met up with next.
BECKETT: Dumais? Who’d she run into?
(Zelenka lowers his head for a moment, then looks at Rodney.)
McKAY: Me. She ran into Hays ... and me. We’re next.

CORRIDOR. Peterson gets another door open. As he walks through, John and Teyla are waiting on the other side. Both of them are armed.
SHEPPARD: Doctor Peterson, I presume.
PETERSON (raising his hands): I’m not going back there.
SHEPPARD: You don’t have much of a choice. (Peterson starts to back away, looking back the way he came for an escape route.) Easy.
PETERSON: I go back there, I get infected, that’s murder.
TEYLA: Once we ensure that you are not infected, you will be allowed back into the city. Until then, you are a threat to the rest of the population.
PETERSON: You won’t shoot a member of your own team. (He lowers his hands and starts to walk towards John and Teyla.)
SHEPPARD: Peterson. (He raises his P90. Peterson stops and raises his hands again.) You will not be allowed to go back to the city.
PETERSON: OK, wait, wait, wait a second. Take me back to the medlab, just quarantine me there. I’ll go voluntarily – just please don’t make me go back there. (He indicates the direction he just came from.)
(John and Teyla look at each other.)
PETERSON: Really, I’m-I’m fine. (He lowers his hands and tries to look calm.) I’m fine. I feel perfectly fine.
SHEPPARD (into radio): Doctor Weir, this is Sheppard. Peterson has agreed to go back to the medlab until we can get this situation resolved.
(While he’s talking, Peterson looks around and sees a transporter room just feet away, and the door is open. He runs towards it.)
SHEPPARD: Stop!
(As Peterson hurls himself into the transporter room, John fires several short bursts from his P90 at the transporter doors to try to stop them from closing but to no avail. At least one of the bullets hits Peterson in the arm, who cries out and collapses to the floor just as the doors finish closing.)
(The transporter doors open again and Peterson hauls himself painfully to his feet and stumbles out ... into the Mess Hall. Clutching his injured arm, he staggers up some steps, groaning, then collapses to the floor. Everybody rushes over to him.)
MAN 1: My God, is he alright?
WOMAN 1: Oh, my God!
MAN 2: He’s been shot!
WOMAN 2: What’s going on?
(There is general hubbub as they carefully turn him over onto his back. Suddenly an alarm starts sounding over the comm system.)
(Back in the corridor, John and Teyla rush into the transporter room but just as John reaches for the control panel, a hatch closes over it. The alarm continues to sound.)
(In the Mess Hall, a similar hatch closes over the transporter room control panel and the doors close. All the exit doors start to close.)
(In the Control Room, the doors are closing on all levels as the alarm continues.)
WEIR: What’s going on?
GRODIN (trying to work his console): Ancient controls are unresponsive.
BATES: I’m getting reports that Peterson transported into the Mess Hall.
SHEPPARD (from the transporter room): For some reason, we can’t follow him.
GRODIN: The city has taken over – put us into a lockdown.
WEIR: Override it.
GRODIN: I can’t! Atlantis must be designed to respond to outbreaks automatically. The city initiated a lockdown when Peterson transported out of the east side.
WEIR: Why now? Why not when Johnson and Wagner became infected?
GRODIN: The city’s detection systems might have been affected by the flooding in those areas. Once Peterson entered the Mess Hall, the pathogen was almost instantly detected by automated systems and the city protected itself.
WEIR: Alright, what are my options?
GRODIN: Limited. As of now, we’re completely locked out of the mainframe.

ANCIENT LAB. Rodney and Hays are being hooked up to heart and blood pressure monitors.
McKAY: Is this really necessary? I am about to die of a brain aneurysm – how does being attached to a heart monitor help?
BECKETT: If you die like the others, we’ll have a better idea of how. (He smiles sarcastically.)
McKAY: At that point, I will cease to care.
FORD: There are a lot of other people that live in the city, man.
McKAY: Yes, the living.

CORRIDORS. John and Teyla are walking along. As they walk past a door, it opens automatically.
SHEPPARD: Thought we were in a lockdown? Why’d that open up for us? (Into radio) Weir, this is Sheppard. Were you able to get the transporters online or not?
(Elizabeth looks round at Peter, who shakes his head.)
WEIR: Doesn’t look promising. Atlantis itself seems to have somehow sensed a threat and taken over most of the controls.
SHEPPARD: So it shut down the transporters?
WEIR: That’s right.
SHEPPARD: Well, I wish we would’ve thought of that.
WEIR (furiously): We did think of that, Major. That entire section had to be powered up for you to open the door to Peterson. In fact, if you hadn’t gone after him, he wouldn’t have been able to use the transporters. D’you still feel it was a good idea?
SHEPPARD: Where’d he transport to?
WEIR: The Mess Hall. Thankfully everyone else respected the quarantine – there’s only a handful of people there.
SHEPPARD: Alright, you’ve made your point.
WEIR: Make your way back to the city. Wait in Beckett’s lab for further instructions.

FIELD STATION. Doctor Biro has finished her autopsy of Dumais.
BIRO (into radio): Doctor Beckett.
BECKETT (over radio): Any progress, Doctor Biro?
BIRO: Just finished Dumais’ autopsy. Would it surprise you to learn she died of a ruptured brain aneurysm above the visual cortex, sir?
BECKETT: No, it wouldn’t. Thank you, Doctor.
BIRO: Didn’t think so.
BECKETT (to Rodney): You know, the position of the rupture could explain your visions. Swelling in that area before the breakage could absolutely account for the hallucinations.
McKAY: I’m no MD but wouldn’t brain swelling on the visual cortex just mean that we experience washes of colour or weird visual anomalies?
BECKETT: It would depend on the person.
McKAY: Yeah, that’s my point. All of our visions are so similar. If they’re the result of arterial swelling, wouldn’t the visions we experience be more random?
BECKETT: Most likely, yeah.
McKAY: Well, the things we’re seeing are pretty damn identical!
(Behind them, the beep rate on Hays’ heart monitor begins to speed up.)
BECKETT: And you think it might have something to do with the nature ...
McKAY: There’s a good chance ...
HAYS: No! Noooo! (He starts slapping at himself, trying to get something off him. A couple of medics try to restrain him.)
McKAY: Hey! It’s not real, remember? It’s not real!
HAYS: No! No! (He continues to flail at the unseen ghosts. His heart rate increases drastically.) They’re coming right at us! Can’t you see them?! (He struggles with the medics who are trying to restrain him. He starts to fall to the floor.)
BECKETT: [Transcriber’s note: Sorry, but I really cannot work out what he says here!]
McKAY: Don’t say fine – he’s not fine! Do something!
BECKETT: There’s nothing to do!
(Abruptly, Hays’ rapid heartbeat stops altogether and the monitor emits a single long tone. Carson rushes over to Hays and starts to administer CPR as a medic puts an airbag over Hays’ nose and mouth.)
BECKETT (counting chest compressions): One, two, three, four, five. (He stops, and the medic pumps air into Hays’ lungs. Carson starts compressions again.) One, two, three, four, five.
McKAY (angrily): Stop! It’s not his heart. Just ... (his voice fades into grief) stop.
(Carson and his team stop their work. The medic lifts away the airbag from Hays’ face and we see that he too has blood coming out of his mouth and nose. Carson stands up and turns to face Rodney, whose expression is one of resignation combined with fear. A medic turns off Hays’ heart monitor. Nearby, members of Rodney’s team are clustered together for comfort. One of the women is in tears. Aidan looks at Rodney.)
FORD: How are you feeling?
McKAY: I’m ... I’m ... Listen, I have a sister. We’re not close – I don’t even know how you’d find her.
FORD: Don’t talk like that.
McKAY: She’s the only family I really have, so someone should tell her what happened. And, uh, make it sound good, OK? (He allows himself a small smile for a moment.) Tell her I ... I died saving someone ... kids! I died saving kids – a bunch of them. Nelenka ... (Zelenka shrugs at Rodney getting his name wrong again, but says nothing.) I’ve got some theories on looping the power on the Gate to charge a dummy ZedPM. It probably won’t work but-but you should have someone look at it cos it might lead somewhere else.
ZELENKA: We’ll look at it together.
McKAY (angry, but also on the verge of tears): Look, you seriously have to stop interrupting my last thoughts. I mean, this is important stuff you need to hear. (He looks round and sees that he has got everybody’s attention. Zelenka nods at him to continue.) Now – if you’re here for more than a year, I’ve left some notes on how to roll blackouts to effectively maintain your power requirements and-and, oh, tell everyone that I was, I was inches away from a Theory of Unification but uh, uh, the notes, they were lost when I died saving the ...
ZELENKA: ... kids.
McKAY: Yeah. (He pauses and looks around the room, expecting the ghostly visions to start. He turns around slowly and stares towards the ceiling, but still the ghosts don’t come. After a long moment ...) OK. I should be dead now.
(Carson walks over to him.)
BECKETT: You ran into Dumais at the same time?
McKAY: Exactly the same time.
BECKETT: Then, yes, you should be dead.
McKAY (looking around as he realises that he isn’t dead): Oh, God! (He looks round at Ford and Zelenka.) I’m still here! (He smiles in disbelieving delight.)
FORD: Yes you are.
ZELENKA: Interesting.
McKAY: “Interesting”?!
BECKETT: Don’t take this the wrong way, but ...
ZELENKA: ... why?
BECKETT: Exactly.
McKAY: Well, I don’t care. (He turns to Carson and smiles in relief.) I mean, I really don’t care!
(Carson smiles and pats him on the arm.)

CONTROL ROOM. The place is a hive of activity as various technicians use laptops to try to hack back into the mainframe. Elizabeth is watching all the hubbub as John reports in over the radio.
SHEPPARD: Doctor Weir?
WEIR: Yes, Major?
SHEPPARD: We’ve reached the city, but we haven’t hit the city’s quarantine. Are you sure it’s locked you out?
WEIR: Pretty sure. I can’t even get into my office.
SHEPPARD: Hasn’t given us any trouble yet.
GRODIN (suddenly realising something): Hazmat suits – they’re protected.
WEIR: What?
GRODIN: The city must be capable of sensing they’re in no danger of infection. It makes sense, actually – this way, Atlantis allows protected personnel to assist the infected.
TEYLA: If that is the case, we should make our way to the Mess Hall. I imagine everyone there will be very scared and confused.
WEIR: I agree. Get to the Mess Hall and report back.

FIELD STATION. Doctor Biro and her team are conducting an autopsy on Hays. Carson and Rodney stand nearby.
BECKETT: Are you certain you really wanna see this, Rodney?
McKAY: It’s too accurate. How could something organic be that efficient?
BECKETT: Again, we’re in the middle of another galaxy. Just because it’s out of the ordinary for us doesn’t mean it’s not commonplace here.
McKAY: No, no, no, I don’t buy that. Most of the habitable planets we’ve encountered thus far are-are-are carbon copies of Earth in terms of environmental conditions. (Carson nods his agreement. Rodney is then struck by a thought and snaps his fingers a couple of times.) Unless ... (He rushes off.)
BECKETT (to the autopsy team): I’ll be back. (He hurries off after Rodney.) Wait up, Rodney!

ANCIENT LAB. Rodney has led Carson back to the lab.
McKAY: Incubation to completion is exactly six hours. The visions are identical for all the infected, and the location of the aneurysm is the same for every single deceased. (He opens up a laptop and shows Carson a display. Carson stares at it in dread.)
BECKETT: Is that what I think it is?
McKAY: It’s a nanovirus. One manufactured to kill humans.

LATER. Rodney is reporting to Elizabeth via radio.
WEIR: A nanovirus.
McKAY: That’s right.
WEIR: OK, let’s pretend I don’t know exactly what that is.
McKAY: Nanotechnology – it’s, uh, technology that operates on a nanite scale. It’s around, uh, around a billionth of a millimetre.
BECKETT: Basically, they’re microscopic machines that are able to carry out very specific tasks suited for their size.
McKAY: It’s the whole idea of being able to swallow a pill and having a million little robots go to work and cure whatever ails you.
WEIR: You’re all infected with microscopic machines?
McKAY: Yeah, they’re no bigger than a single-celled organism – although instead of having a sole purpose of curing a disease or mending a blood vessel ...
BECKETT: ... the virus is programmed to terrorise its victims by tapping into their visual cortex and then rupturing an artery in their brain ...
McKAY: ... infecting others along the way as they can.
BECKETT: There’s one good thing: I doubt they can multiply. I don’t know how many nanites it takes to kill a human but eventually I imagine they’ll spread themselves too thin.
WEIR: Could it be Wraith?
BECKETT: That would definitely be my first guess.
McKAY: I’m not so sure about that.
BECKETT: But the visions; the shrill sound you told me they make when they ...
McKAY: I’ll give you that they’re equally terrifying, but why would the Wraith even create the equivalent of a WMD? They’re killing us, not because they sadistically want us dead, but because they need to consume us for food. Look – it would be like the equivalent of cattle farmers creating mad cow disease. I don’t buy it.
WEIR: You did come across it in an Ancient lab.
McKAY: What, so wiping out the Wraith’s food supply was a last-ditch consideration?
BECKETT: I don’t believe that for a moment. The Ancients would never create something like this.
McKAY: It doesn’t explain the visions either.
WEIR: OK, for the moment, who built the virus is really the least of our concerns.
McKAY: Good point.

MESS HALL. John and Teyla have arrived. John is looking at Peterson’s body, which is lying on a table with blood coming from his nose. Teyla is trying to explain the situation to the others.
TEYLA: We have yet to determine how one contracts the virus. It is very possible that none of you have been infected.
LIEUTENANT CROWN: Then why are you in hazmat suits?
TEYLA: Just as a precaution.
(Rodney contacts John by radio.)
McKAY: Major Sheppard, this is McKay.
SHEPPARD: What is it?
McKAY: I could use your help at my lab.
(John looks round at Teyla, who is being bombarded with nervous questions.)
TEYLA: Go. I will be fine.
(John leaves. The others cluster round Teyla, still firing questions at her.)

LATER. Rodney and Carson are explaining things to Elizabeth.
McKAY: Hays and I were infected at the same time. There’s only one thing that explains why I survived.
BECKETT: Rodney has the Ancient gene; Hays did not.
WEIR: But Rodney is not an Ancient.
BECKETT: Aye, but he’s been inoculated with the ATA gene.
WEIR: You’re saying the virus is designed to only kill humans?!
McKAY: Well, I’m human!
BECKETT: Yes, yes, we’re making a point, Rodney.
WEIR: So we give everyone the gene therapy.
McKAY: No – it’s not gonna do it.
ZELENKA: I’ve already been given the gene weeks ago – it didn’t take.
McKAY: I know. I’m already on it.
ZELENKA: The gene therapy is only effective in forty-eight percent of recipients.
FORD (to Beckett): If I was given the gene shot right now, how long would it take to kick in?
BECKETT: A minimum of four hours.
FORD: I don’t have four hours! I met up with McKay and Hays ninety minutes after they met up with Dumais. I have (he checks his watch) a little under an hour before my brain explodes.
BECKETT: Aidan, listen to me. You’ve been up for almost twenty hours now – you’re not thinking straight. Just try to stay calm.
FORD: Calm?! You told me I have a million tiny robots running through my veins whose only purpose is to terrorise and kill me. You stay calm!
ZELENKA: We are about to have hallucinations. We are infected, Carson – how do you expect us to act?!
FORD: There’s gotta be another way.
McKAY: I have already told you – I am working on it.

LATER. John has reached Rodney’s lab.
SHEPPARD: Alright, McKay, I’m here.
McKAY: D’you see it?
SHEPPARD: Is it the big thing in the middle of the room?
McKAY: Yeah, that’s the one.
(We see part of the piece of equipment that John is looking at – it is covered with yellow and black hazard strips, together with “Warning” and “Caution” stickers.)
SHEPPARD: Should I pay attention to all these warnings?
McKAY: Not today, no.
(The camera pulls back and we see that the device is an EM pulse generator [though it’s smaller than the one we last saw Rodney playing with in the SG-1 episode “Redemption part 2”].)
FORD: What are you gonna do?
McKAY: Well, small as they are, the nanovirus is still effectively just a machine run by a computer. The best way to knock out a computer is with an electromagnetic pulse. Thankfully, that’s something we can do.
(In the Control Room, the technicians are shutting down all the laptops and disconnecting them from the mainframe.)
WEIR: We’re about through shutting down all the electronic gear we brought from Earth. We’re still locked out of the Ancient controls, though. There’s no way to power them down.
McKAY: Well, it’s not gonna be necessary. Ancient technology works differently than ours. An EM pulse shouldn’t have any long-lasting effect on ‘em.
GRODIN: We’re ready.
WEIR: We’re all set, Rodney.
McKAY: OK. Here we go.
WEIR: Wait! How’re we gonna know if it works?
SHEPPARD: Well, Sheppard’s dialling up the most powerful pulse the generator can manage. It probably won’t make it all the way down here but it should affect most of the central tower. I imagine once it wipes out the virus, the city should return control of it to you and end the lockdown.
FORD: It won’t make it here?
McKAY: If the pulse works, it will simply be a matter of walking you down to my lab, sitting you down in front of the EMP and repeating the process. (Into radio) Major?
SHEPPARD: It’s working. (We see that the generator is spinning up to speed.) When should I hit the discharge button?
McKAY: OK – there should be a red overload light.
SHEPPARD: Yeah, I see it.
McKAY: Wait til it comes on, give it a good ten count, and then discharge.
SHEPPARD: A ten count?!
McKAY: Don’t worry – I’ve probably been around more EMPs than anyone.
SHEPPARD: This is gonna be, uh – I’m gonna be fine, right?
McKAY (rather sarcastically): Yes. That’s a yes – you’ll be fine.
(In Rodney’s lab, the overload light comes on. John flips open the cover to the discharge button, moving his lips as he silently counts off the seconds. Then he pushes the button. The generator whooshes as it discharges.)
(In the Ancient lab, Rodney is waiting impatiently.)
(In Rodney’s lab, the generator is powering down, then stops. John looks around expectantly.)
(In the Control Room, everyone is waiting.)
McKAY (over comms): Anything?
WEIR: Is it possible it might take some time?
McKAY (sighing): Doubtful.
(Peter turns to his console and starts trying to active it.)
McKAY: Are you still locked out of the Ancient mainframe?
(Peter turns to the screen that shows the mainframe, but there’s no response from it. He turns to Elizabeth and shakes his head.)
WEIR (to Rodney): Got any other ideas?
(Rodney has no reply. Aidan checks his watch anxiously.)
FORD: Twenty-nine minutes.

MESS HALL. The people locked in there are either milling around talking with each other or sitting at the tables. Suddenly one of the marines sitting down looks up in terror, jumps to his feet and starts backing away, whimpering and terrified. Almost immediately, everyone else in the room starts reacting to his or her own visions. Chaos reigns as they all run around the roam, flailing at the ghosts they think are attacking them. Lieutenant Crown runs over to Teyla.
CROWN: It didn’t work! It didn’t work!
TEYLA: It is still unclear.
CROWN: What’s unclear? Either it worked or it didn’t!
TEYLA: They are trying to determine ... (She trails off as Crown stares at her in terror.)
CROWN: They’re everywhere!
TEYLA: You are experiencing a hallucination.
(Crown starts flailing at Teyla, trying to get the ghosts away from herself. She pushes Teyla over the top of a table. Glass smashes as the table falls over, then Crown and Teyla crash down on top of the broken glass. Teyla tosses Crown away from herself, then looks down and realises that the arm of her hazmat suit is gashed and her arm is exposed to the air.)
CROWN (seeing what she’s done): Oh, my God!

RODNEY’S LAB. John has apparently been following some instructions from Rodney.
SHEPPARD: I’ve already tried that – it’s blown.
McKAY: That is before we re-set the sub-switch.
SHEPPARD: Well, maybe we shouldn’t have overloaded it so much.
McKAY: Look, it’s fixable, it’s fixable – we just need to use a little trial and error.
SHEPPARD: Look, even if we get this thing working, who’s to say the pulse is gonna get any bigger? Ford and Zelenka have twenty minutes before their arteries rupture. Are you sure an EMP will kill this thing?
McKAY: Yes.
SHEPPARD: Alright. I have an idea. (He hurries out of the lab.)

GENERATOR ROOM. John has gone to where one of the naqahdah generators is running.
SHEPPARD (into radio): What do you mean, no?
WEIR: It’s too dangerous.
SHEPPARD: You’d rather lose a third of our population?
WEIR: We’re not there yet, Major.
SHEPPARD: We are there! Ford and Zelenka are next. The people in the Mess Hall have a little over three hours. This is a full-blown outbreak. People are gonna keep dying unless we do this.
McKAY: Even if we were able to get the EMP generator back online, the chances are slim that we would ever be able to get it powerful enough.
WEIR: Can we bring the infected to the generator?
GRODIN: We can’t. The city won’t let infected personnel through any of the doors.
McKAY: The major is right – the only way to create an EMP strong enough to wipe these little guys out is to ...
WEIR: ... to detonate a nuclear explosion in the atmosphere! Yes, I heard the first time!
McKAY: I know it sounds severe but if the major was able to overload a naqahdah generator twenty miles above the city, it would be perfectly safe from a radiological standpoint and the ensuing blast would be capable of creating a devastating electromagnetic shockwave – definitely enough to knock this virus out.
GRODIN: Hopefully without destroying all our own computer equipment!
SHEPPARD: It’s worth the risk.
(Elizabeth thinks about it for a moment.)
WEIR (somewhat reluctantly): OK. You have a go.
(John lifts the control mechanism on the top of the naqahdah generator, twists it through ninety degrees and lowers it back down into place. The generator shuts down. John detaches its connecting cables, closes the generator down to make it more compact, lifts it up and carries it away.)

JUMPER BAY. John takes off in one of the Puddlejumpers.

LATER. PUDDLEJUMPER.
SHEPPARD: I’m almost in position.
WEIR: Understood. Would the EM pulse have any effect on the Puddlejumper?
SHEPPARD: I’m hoping not. Either way, I’m more worried about the shockwave.
WEIR: Good luck.
SHEPPARD: You too.
McKAY: You’re only gonna have thirty seconds once you release it before it explodes. You need to get as far away as you can.
SHEPPARD: Get as far away from the nuclear explosion as possible – that’s good advice, Rodney, thanks!
McKAY: You’re welcome.
SHEPPARD: I’m releasing the generator ... now!
(Twenty miles above the planet’s surface, the naqahdah generator is jettisoned out of the top of the Puddlejumper. The Jumper immediately goes into a steep dive and heads away from the generator.)

PUDDLEJUMPER. John is racing to get away from the impending explosion. He looks very scared.
GRODIN: ... five, four, three, two, one.

ABOVE THE PLANET. The naqahdah generator explodes. The Puddlejumper is buffeted violently by the enormous shockwave.

ATLANTIS. Above the city, the night sky turns a brilliant white. All around the base, anybody near a window flinches away from the light.

CONTROL ROOM. The light fades.
WEIR: Major Sheppard, come in. (No response.) This is Weir – please respond.
GRODIN: Communications may have been disrupted by the blast.
WEIR: Major, do you read me? (There is no response.)
(All around the base, people look concerned. Finally, after several seconds ...)
SHEPPARD: This is Sheppard. I’ve cleared the blast – I’m returning home.
WEIR: I’m glad to hear it, Major.
SHEPPARD: Did it work?
WEIR: We’re about to find out. (She walks over to Peter, who activates controls on his console, then turns anxiously towards the mainframe screen. After a moment, the screen flashes.)
McKAY: You should know almost right away.
(In the Control Room, doors start to open. The technicians run to their laptops and start opening them.)
McKAY: The pulse only lasts a couple of microseconds and then ...
WEIR: The city’s already ahead of us, Rodney. You have a green light to return.
(In the Ancient lab, Rodney claps his hands together in relief. Various team members hug each other. Rodney shakes hands with Zelenka. Aidan and Carson hug, then Aidan goes over to Rodney and hugs him too.)

LATER. WEIR’S OFFICE. Elizabeth and John are in there.
WEIR: Are you OK?
SHEPPARD: Yeah, just a little nuke – nothin’, really.
WEIR: The naqahdah generator plan was very clever. Good work.
SHEPPARD: Thank you. Now, I’m going to bed. (He stands up to leave.)
WEIR: We need to discuss what happened earlier.
SHEPPARD (turning round wearily): Now?
WEIR: That can never happen again.
(John looks at her for a moment, then comes back to the desk and sits down.)
SHEPPARD: Look, I’m sorry about ...
WEIR (interrupting): I understand your expertise in military matters and I agree that I should defer to those expertise in such situations.
SHEPPARD: Thank you!
WEIR: But you are not the one who decides what is and what is not a military situation. Now, both General O’Neill and Colonel Sumner warned me that you don’t respect the proper chain of command.
SHEPPARD: Well, sometimes I see a situation a little different than ...
WEIR: No. Listen to me, John. Now, you endangered yourself and the lives of many others.
SHEPPARD: Because I thought it was the best course of action to take – and, by the way, I saved your ass.
WEIR: I know you did – but you have to trust me.
SHEPPARD: I do!
WEIR: Do you?
(Rodney and Carson come in.)
McKAY: You guys have a minute? We’ve been able to spend some, uh, quality time with the, uh, nanovirus samples.
BECKETT: From what we can tell, they’ve all been incapacitated.
WEIR: Well, that’s good news.
McKAY: Yes. Also, upon further investigation, I think we can rule out that they were created by the Wraith. They’re different than any Wraith technology we’ve come across thus far.
SHEPPARD: If not the Wraith, then who made ‘em?
McKAY: I honestly don’t know – but whoever they were, let’s just hope that they’re not still around.
WEIR: Let’s hope.